Search results for: Functional response

Authors: F. Fekak, A. Gravouil, M. Brun, B. Depale

Abstract:

During an earthquake, a bridge crane may be subjected to multiple impacts between crane wheels and rail. In order to model such phenomena, a time-history dynamic analysis with a multi-scale approach is performed. The high frequency aspect of the impacts between wheels and rails is taken into account by a Lagrange explicit event-capturing algorithm based on a velocity-impulse formulation to resolve contacts and impacts. An implicit temporal scheme is used for the rest of the structure. The numerical coupling between the implicit and the explicit schemes is achieved with a heterogeneous asynchronous time-integrator.

Keywords: Earthquake, bridge crane, heterogeneous asynchronous time-integrator, impacts.

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Authors: Towfeeq Fairooz, Salim Istyaq

Abstract:

The passive electrical properties of a tissue depends on the intrinsic constituents and its structure, therefore by measuring the complex electrical impedance of the tissue it might be possible to obtain indicators of the tissue state or physiological activity [1]. Complete bio-impedance information relative to physiology and pathology of a human body and functional states of the body tissue or organs can be extracted by using a technique containing a fourelectrode measurement setup. This work presents the estimation measurement setup based on the four-electrode technique. First, the complex impedance is estimated by three different estimation techniques: Fourier, Sine Correlation and Digital De-convolution and then estimation errors for the magnitude, phase, reactance and resistance are calculated and analyzed for different levels of disturbances in the observations. The absolute values of relative errors are plotted and the graphical performance of each technique is compared.

Keywords: Electrical Impedance, Fast Fourier Transform, Additive White Gaussian Noise, Total Least Square, Digital De-Convolution, Sine-Correlation.

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Authors: M. Vesali Naseh, A. A. Khodadadi, Y. Mortazavi, O. Alizadeh Sahraei, F. Pourfayaz, S. Mosadegh Sedghi

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In this study, multiwall carbon nanotubes (MWNTs) were modified with nitric acid chemically and by dielectric barrier discharge (DBD) plasma in an oxygen-based atmosphere. Used carbon nanotubes (CNTs) were prepared by chemical vapour deposition (CVD) floating catalyst method. For removing amorphous carbon and metal catalyst, MWNTs were exposed to dry air and washed with hydrochloric acid. Heating purified CNTs under helium atmosphere caused elimination of acidic functional groups. Fourier transformed infrared spectroscopy (FTIR) shows formation of oxygen containing groups such as C=O and COOH. Brunauer, Emmett, Teller (BET) analysis revealed that functionalization causes generation of defects on the sidewalls and opening of the ends of CNTs. Results of temperature-programmed desorption (TPD) and gas chromatography(GC) indicate that nitric acid treatment create more acidic groups than plasma treatment.

Keywords: Carbon nanotubes (CNTs), chemical treatment, functionalization, plasma.

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Authors: Nicolò Vaiana, Filip C. Filippou, Giorgio Serino

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The solution of the nonlinear dynamic equilibrium equations of base-isolated structures adopting a conventional monolithic solution approach, i.e. an implicit single-step time integration method employed with an iteration procedure, and the use of existing nonlinear analytical models, such as differential equation models, to simulate the dynamic behavior of seismic isolators can require a significant computational effort. In order to reduce numerical computations, a partitioned solution method and a one dimensional nonlinear analytical model are presented in this paper. A partitioned solution approach can be easily applied to base-isolated structures in which the base isolation system is much more flexible than the superstructure. Thus, in this work, the explicit conditionally stable central difference method is used to evaluate the base isolation system nonlinear response and the implicit unconditionally stable Newmark’s constant average acceleration method is adopted to predict the superstructure linear response with the benefit in avoiding iterations in each time step of a nonlinear dynamic analysis. The proposed mathematical model is able to simulate the dynamic behavior of seismic isolators without requiring the solution of a nonlinear differential equation, as in the case of widely used differential equation model. The proposed mixed explicit-implicit time integration method and nonlinear exponential model are adopted to analyze a three dimensional seismically isolated structure with a lead rubber bearing system subjected to earthquake excitation. The numerical results show the good accuracy and the significant computational efficiency of the proposed solution approach and analytical model compared to the conventional solution method and mathematical model adopted in this work. Furthermore, the low stiffness value of the base isolation system with lead rubber bearings allows to have a critical time step considerably larger than the imposed ground acceleration time step, thus avoiding stability problems in the proposed mixed method.

Keywords: Base-isolated structures, earthquake engineering, mixed time integration, nonlinear exponential model.

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Authors: Jafar Ahmadi, Nafiseh Noormohammadi, Sedigheh Fabriki Ourang

Abstract:

GRF, Growth regulating factor, genes encode a novel class of plant-specific transcription factors. The GRF proteins play a role in the regulation of cell numbers in young and growing tissues and may act as transcription activations in growth and development of plants. Identification of GRF genes and their expression are important in plants to performance of the growth and development of various organs. In this study, to better understanding the structural and functional differences of GRFs family, 45 GRF proteins sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H. vulgare and S. bicolor, have been collected and analyzed through bioinformatics data mining. As a result, in secondary structure of GRFs, the number of alpha helices was more than beta sheets and in all of them QLQ domains were completely in the biggest alpha helix. In all GRFs, QLQ and WRC domains were completely protected except in AtGRF9. These proteins have no trans-membrane domain and due to have nuclear localization signals act in nuclear and they are component of unstable proteins in the test tube.

Keywords: Domain, Gene Family, GRF, Motif.

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Authors: Sadílek M., Čep R.

Abstract:

This work deals with problems of tool axis inclination angles in ball-end milling. Tool axis inclination angle contributes to improvement of functional surface properties (surface integrity - surface roughness, residual stress, micro hardness, etc.), decreasing cutting forces and improving production. By milling with ball-end milling tool, using standard way of cutting, when work piece and cutting tool contain right angle, we have zero cutting speed on edge. At this point cutting tool only pushes material into the work piece. Here we can observe the following undesirable effects - chip contraction, increasing of cutting temperature, increasing vibrations or creation of built-up edge. These effects have negative results – low quality of surface and decreasing of tool life (in the worse case even it is pinching out). These effects can be eliminated with the tilt of cutting tool or tilt of work piece.

Keywords: CAD/CAM system, tool axis inclination angle, ballend milling, surface roughness, cutting forces.

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Authors: I. Ioannou, I. M. Gitman

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This study focused on the contribution of micro-mechanical parameters on the macro-mechanical response of short fiber composites, namely polypropylene matrix reinforced by glass fibers. In the framework of this paper, an attention has been given to the glass fibers length, as micromechanical parameter influences the overall macroscopic material’s behavior. Three dimensional numerical models were developed and analyzed through the concept of a Representative Volume Element (RVE). Results of the RVE-based approach were compared with analytical Halpin-Tsai’s model.

Keywords: Effective properties, representative volume element, short fiber reinforced composites.

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Authors: Parisa Farzaneh, Azade Harati

Abstract:

Mushrooms or macro-fungi, as an important superfood, contain many bioactive compounds, particularly bio-peptides. In this research, mushroom proteins were extracted by buffer or buffer plus salt (0.15 M), along with ultrasound bath to extract the intercellular protein. As a result, the highest amount of proteins in mushrooms were categorized into albumin. Proteins were also hydrolyzed and changed into peptides through endogenous and exogenous proteases, including gastrointestinal enzymes. The potency of endogenous proteases was also higher in Agaricus bisporus than Terfezia claveryi, as their activity ended at 75 for 15 min. The blanching process, endogenous enzymes, the mixture of gastrointestinal enzymes (pepsin-trypsin-α-chymotrypsin or trypsin- α-chymotrypsin) produced the different antioxidant and antibacterial hydrolysates. The peptide fractions produced with different cut-off ultrafilters also had various levels of radical scavenging, lipid peroxidation inhibition, and antibacterial activities. The bio-peptides with the superior bio-activities (less than 3 kD of T. claveryi) were resistance to various environmental conditions (pH and temperatures). Therefore, they are good options to be added in nutraceutical and pharmaceutical preparations or functional foods, even during processing. 

Keywords: Bio-peptides, mushrooms, gastrointestinal enzymes, bioactivities.

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Authors: Kamil Aida-zade, C. Ardil

Abstract:

We study the problem of synthesis of lumped sources control for the objects with distributed parameters on the basis of continuous observation of phase state at given points of object. In the proposed approach the phase state space (phase space) is beforehand somehow partitioned at observable points into given subsets (zones). The synthesizing control actions therewith are taken from the class of piecewise constant functions. The current values of control actions are determined by the subset of phase space that contains the aggregate of current states of object at the observable points (in these states control actions take constant values). In the paper such synthesized control actions are called zone control actions. A technique to obtain optimal values of zone control actions with the use of smooth optimization methods is given. With this aim, the formulas of objective functional gradient in the space of zone control actions are obtained.

Keywords: Feedback control, distributed systems, smooth optimization methods, lumped control synthesis.

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Authors: Sean Paulsen, Michael Casey

Abstract:

In this work, we present a self-supervised pretraining framework for transformers on functional Magnetic Resonance Imaging (fMRI) data. First, we pretrain our architecture on two self-supervised tasks simultaneously to teach the model a general understanding of the temporal and spatial dynamics of human auditory cortex during music listening. Our pretraining results are the first to suggest a synergistic effect of multitask training on fMRI data. Second, we finetune the pretrained models and train additional fresh models on a supervised fMRI classification task. We observe significantly improved accuracy on held-out runs with the finetuned models, which demonstrates the ability of our pretraining tasks to facilitate transfer learning. This work contributes to the growing body of literature on transformer architectures for pretraining and transfer learning with fMRI data, and serves as a proof of concept for our pretraining tasks and multitask pretraining on fMRI data.

Keywords: Transfer learning, fMRI, self-supervised, brain decoding, transformer, multitask training.

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Authors: A. Chellil, A. Nour, S. Lecheb, H. Mechakra, A. Bouderba, H. Kebir

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In this paper, a coupled damage effect in the instability of a composite rotor is presented, under dynamic loading response in the harmonic analysis condition. The analysis of the stress which operates the rotor is done. Calculations of different energies and the virtual work of the aerodynamic loads from the rotor blade are developed. The use of the composite material for the rotor offers a good stability. Numerical calculations on the model developed prove that the damage effect has a negative effect on the stability of the rotor. The study of the composite rotor in transient system allowed determining the vibratory responses due to various excitations.

Keywords: Rotor, composite, damage, finite element, numerical.

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Authors: S. K. Madan, R. S. Malik, V. K. Sehgal

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R.C.C. buildings with dual structural system consisting of shear walls (or braces) and moment resisting frames have been widely used to resist lateral forces during earthquakes. The dual systems are designed to resist the total design lateral force in proportion to their lateral stiffness. The response of combination of braces and shear walls has not yet been studied. The combination may prove to be more effective to resist lateral forces during earthquakes. This concept has been applied to regular R.C.C. buildings provided with shear walls, braces and their combinations.

Keywords: Dynamic analysis, Displacement, Dual structural system, Storey drift.

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Authors: Aye Aye Mon

Abstract:

The application of a simple microcontroller to deal with a three variable input and a single output fuzzy logic controller, with Proportional – Integral – Derivative (PID) response control built-in has been tested for an automatic voltage regulator. The fuzzifiers are based on fixed range of the variables of output voltage. The control output is used to control the wiper motor of the auto transformer to adjust the voltage, using fuzzy logic principles, so that the voltage is stabilized. In this report, the author will demonstrate how fuzzy logic might provide elegant and efficient solutions in the design of multivariable control based on experimental results rather than on mathematical models.

Keywords: Fuzzy logic system, PID Controller, control systems, controlled A V R

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Authors: J. Fernandez de Canete, S. Gonzalez-Perez, P. del Saz-Orozco

Abstract:

LABVIEW is a graphical programming language that has its roots in automation control and data acquisition. In this paper we have utilized this platform to provide a powerful toolset for process identification and control of nonlinear systems based on artificial neural networks (ANN). This tool has been applied to the monitoring and control of a lab-scale distillation column DELTALAB DC-SP. The proposed control scheme offers high speed of response for changes in set points and null stationary error for dual composition control and shows robustness in presence of externally imposed disturbance.

Keywords: Distillation, neural networks, LABVIEW, monitoring, identification, control.

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Authors: Mohammad Saleh Tavazoei, Mohammad Haeri

Abstract:

This paper presents comparison among methods of determination of the characteristic polynomial coefficients. First, the resultant systems from the methods are compared based on frequency criteria such as the closed loop bandwidth, gain and phase margins. Then the step responses of the resultant systems are compared on the basis of the transient behavior criteria including overshoot, rise time, settling time and error (via IAE, ITAE, ISE and ITSE integral indices). Also relative stability of the systems is compared together. Finally the best choices in regards to the above diverse criteria are presented.

Keywords: Characteristic Polynomial, Transient Response, Filters, Stability.

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Authors: Yousra M. Zakaria Helmy, Edward H. Smith

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Lake Nasser is one of the largest reservoirs in the world. Over 120 million metric tons of sediments are deposited in its dead storage zone every year. The main objective of the present work was to determine the physical and chemical characteristics of Lake Nasser sediments. The sample had a relatively low surface area of 2.9 m2/g which increased more than 3-fold upon chemical activation. The main chemical elements of the raw sediments were C, O and Si with some traces of Al, Fe and Ca. The organic functional groups for the tested sample included O-H, C=C, C-H and C-O, with indications of Si-O and other metal-C and/or metal-O bonds normally associated with clayey materials. Potentiometric titration of the sample in different ionic strength backgrounds revealed an alkaline material with very strong positive surface charge at pH values just a little less than the pH of zero charge which is ~9. Surface interactions of the sediments with the background electrolyte were significant. An advanced surface complexation model was able to capture these effects, employing a single-site approach to represent protolysis reactions in aqueous solution, and to determine the significant surface species in the pH range of environmental interest.

Keywords: Lake Nasser, sediments, surface characterization

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Authors: R. Hashemi, M.H.Kargarnovin

Abstract:

This paper presents the identification of the impact force acting on a simply supported beam. The force identification is an inverse problem in which the measured response of the structure is used to determine the applied force. The identification problem is formulated as an optimization problem and the genetic algorithm is utilized to solve the optimization problem. The objective function is calculated on the difference between analytical and measured responses and the decision variables are the location and magnitude of the applied force. The results from simulation show the effectiveness of the approach and its robustness vs. the measurement noise and sensor location.

Keywords: Genetic Algorithm, Inverse problem, Optimization, Vibration.

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Authors: Cj Gletus Matthews Cn Jacobs, Kogilah Narayanasamy

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This article explores the sociological perspectives on social problems and the role of the media which has a delicate role to tread in balancing its duty to the public and the victim Whilst social problems have objective conditions, it is the subjective definition of such problems that ensure which social problem comes to the fore and which doesn-t. Further it explores the roles and functions of policymakers when addressing social problems and the impact of the inception of media profiling as well as the advantages and disadvantages of media profiling towards social problems. It focuses on the inception of media profiling due to its length and a follow up article will explore how current media profiling towards social problems have evolved since its inception.

Keywords: Media Profiling, Policy Response, Social Problems

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Authors: Seyed Ali Sedigh Zyabari, A. Zarifkar

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Single photon detectors have been fabricated NbN nano wire. These detectors are fabricated from high quality, ultra high vacuum sputtered NbN thin films on a sapphire substrate. In this work a typical schematic of the nanowire Single Photon Detector structure and then driving and measurement electronic circuit are shown. The response of superconducting nanowire single photon detectors during a photo detection event, is modeled by a special electrical circuits (two circuit). Finally, current through the wire is calculated by solving equations of models.

Keywords: NbN, nanowire meander, superconducting single photon detector, kinetic inductance.

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Authors: D. Singh, R. Yousefi, M. Boroushaki

Abstract:

Intelligent deep-drawing is an instrumental research field in sheet metal forming. A set of 28 different experimental data have been employed in this paper, investigating the roles of die radius, punch radius, friction coefficients and drawing ratios for axisymmetric workpieces deep drawing. This paper focuses an evolutionary neural network, specifically, error back propagation in collaboration with genetic algorithm. The neural network encompasses a number of different functional nodes defined through the established principles. The input parameters, i.e., punch radii, die radii, friction coefficients and drawing ratios are set to the network; thereafter, the material outputs at two critical points are accurately calculated. The output of the network is used to establish the best parameters leading to the most uniform thickness in the product via the genetic algorithm. This research achieved satisfactory results based on demonstration of neural networks.

Keywords: Deep-drawing, Neural network, Genetic algorithm, Sheet metal forming.

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Authors: Inês Ramalhete, Hugo Farias, Rui da Silva Pinto

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Adequate housing has been a widely discussed theme in academic circles related to low-cost housing, whereas its physical features are easy to deal with, overcrowding (related to social, cultural and economic aspects) is still ambiguous, particularly regarding the set of indicators that can accurately reflect and measure it. This paper develops research on low-cost housing models for developing countries and what is the best method to embed overcrowding as an important parameter for adaptability. A critical review of international overcrowding indicators and their application in two developing countries, Cape Verde and Angola, is presented. The several rationales and the constraints for an accurate assessment of overcrowding are considered, namely baseline data (statistics), which can induce misjudgments, as well as social and cultural factors (such as personal choices of residents). This paper proposes a way to tackle overcrowding through housing adaptability, considering factors such as physical flexibility, functional ambiguity, and incremental expansion schemes. Moreover, a case-study is presented to establish a framework for the theoretical application of the proposed approach.

Keywords: Adaptive housing, low-cost housing, overcrowding.

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Authors: Hafizuddin W. Yussof, Syamsutajri S. Bahri, Adam P. Harvey

Abstract:

Strong anion exchange resins with QN+OH-, have the potential to be developed and employed as heterogeneous catalyst for transesterification, as they are chemically stable to leaching of the functional group. Nine different SIERs (SIER1-9) with QN+OH-were prepared by suspension polymerization of vinylbenzyl chloridedivinylbenzene (VBC-DVB) copolymers in the presence of n-heptane (pore-forming agent). The amine group was successfully grafted into the polymeric resin beads through functionalization with trimethylamine. These SIERs are then used as a catalyst for the transesterification of triacetin with methanol. A set of differential equations that represents the Langmuir-Hinshelwood-Hougen- Watson (LHHW) and Eley-Rideal (ER) models for the transesterification reaction were developed. These kinetic models of LHHW and ER were fitted to the experimental data. Overall, the synthesized ion exchange resin-catalyzed reaction were welldescribed by the Eley-Rideal model compared to LHHW models, with sum of square error (SSE) of 0.742 and 0.996, respectively.

Keywords: Anion exchange resin, Eley-Rideal, Langmuir-Hinshelwood-Hougen-Watson, transesterification.

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Authors: Y. Yanagawa, K. Aihara, S. Watanabe, M. Takemoto, T. Naito, T. Iba, H. Tanaka

Abstract:

This study retrospectively investigated the significance of whole body CT (WCT) for patients with sepsis. A medical chart review was retrospectively performed for all patients with systemic inflammatory response syndrome that were treated initially between April 2011 and March 2012. The subjects were divided into a WCT group that underwent WCT on arrival and a control group. Results of this study suggested that WCT for sepsis was useful for elderly patients whose chief complaint or physiological findings could not suggest the anatomical site of infection, to determine the infectious focus and indications/method for surgery, to diagnose the basic diseases associated with opportunistic infections and to evaluate complicated diseases

Keywords: Sepsis, CT, outcome.

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Authors: Mohsen Ebrahimi, Milad M. Rabieh

Abstract:

In this paper, two very different optimization algorithms, Genetic and DIRECT algorithms, are used to history match a bottomhole pressure response for a reservoir with wellbore storage and skin with the best possible analytical model. No initial guesses are available for reservoir parameters. The results show that the matching process is much faster and more accurate for DIRECT method in comparison with Genetic algorithm. It is furthermore concluded that the DIRECT algorithm does not need any initial guesses, whereas Genetic algorithm needs to be tuned according to initial guesses.

Keywords: DIRECT algorithm, Genetic algorithm, Analytical modeling, History match

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Authors: Samy E. Oraby, Ayman M. Alaskari

Abstract:

The importance of machining process in today-s industry requires the establishment of more practical approaches to clearly represent the intimate and severe contact on the tool-chipworkpiece interfaces. Mathematical models are developed using the measured force signals to relate each of the tool-chip friction components on the rake face to the operating cutting parameters in rough turning operation using multilayers coated carbide inserts. Nonlinear modeling proved to have high capability to detect the nonlinear functional variability embedded in the experimental data. While feedrate is found to be the most influential parameter on the friction coefficient and its related force components, both cutting speed and depth of cut are found to have slight influence. Greater deformed chip thickness is found to lower the value of friction coefficient as the sliding length on the tool-chip interface is reduced.

Keywords: Mathematical modeling, Cutting forces, Frictionforces, Friction coefficient and Chip ratio.

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Authors: Nicolò Vaiana, Filip C. Filippou, Giorgio Serino

Abstract:

In order to reduce numerical computations in the nonlinear dynamic analysis of seismically base-isolated structures, a Mixed Explicit-Implicit time integration Method (MEIM) has been proposed. Adopting the explicit conditionally stable central difference method to compute the nonlinear response of the base isolation system, and the implicit unconditionally stable Newmark’s constant average acceleration method to determine the superstructure linear response, the proposed MEIM, which is conditionally stable due to the use of the central difference method, allows to avoid the iterative procedure generally required by conventional monolithic solution approaches within each time step of the analysis. The main aim of this paper is to investigate the stability and computational efficiency of the MEIM when employed to perform the nonlinear time history analysis of base-isolated structures with sliding bearings. Indeed, in this case, the critical time step could become smaller than the one used to define accurately the earthquake excitation due to the very high initial stiffness values of such devices. The numerical results obtained from nonlinear dynamic analyses of a base-isolated structure with a friction pendulum bearing system, performed by using the proposed MEIM, are compared to those obtained adopting a conventional monolithic solution approach, i.e. the implicit unconditionally stable Newmark’s constant acceleration method employed in conjunction with the iterative pseudo-force procedure. According to the numerical results, in the presented numerical application, the MEIM does not have stability problems being the critical time step larger than the ground acceleration one despite of the high initial stiffness of the friction pendulum bearings. In addition, compared to the conventional monolithic solution approach, the proposed algorithm preserves its computational efficiency even when it is adopted to perform the nonlinear dynamic analysis using a smaller time step.

Keywords: Base isolation, computational efficiency, mixed explicit-implicit method, partitioned solution approach, stability.

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Authors: O. S. Saulters, S. D. Goldberg, W. A. Staples, E. I. Martinez, L. M. Sanchez, D. E. Archuleta, D. L. Williams, S. D. Johnson, A. M. Baker

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To address an important set of unverified field conditions, the Los Alamos National Laboratory Waste Compliance and Tracking System (WCATS) Wall-to-Wall Team performed an unprecedented and advanced inventory. This reconciliation involved confirmation analysis for approximately 5850 hazardous, low-level, mixed low-level, and transuranic waste containers located in more than 200 staging and storage areas across 33 Technical Areas. The interdisciplinary team scoped, planned, and developed the multidimensional assessments. Through coordination with cross-functional site hosts, they were able to verify and validate data while resolving discrepancies identified in WCATS. The results were extraordinary with an updated inventory, tailored outreach, more cohesive communications, and timely closed-loop feedbacks.

Keywords: Circular economy, environmental performance data, social-ecological-technological systems, waste management.

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Authors: Le Zhao, Alain Nogaret

Abstract:

We have built universal central pattern generator (CPG) hardware by interconnecting Hodgkin-Huxley neurons with reciprocally inhibitory synapses. We investigate the dynamics of neuron oscillations as a function of the time delay between current steps applied to individual neurons. We demonstrate stimulus dependent switching between spiking polyrhythms and map the phase portraits of the neuron oscillations to reveal the basins of attraction of the system. We experimentally study the dependence of the attraction basins on the network parameters: The neuron response time and the strength of inhibitory connections.

Keywords: Central pattern generator, winnerless competition principle.

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Authors: Soichi Ogishima, Takeshi Hase, So Nakagawa, Yasuhiro Suzuki, Hiroshi Tanaka

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To understand life as biological system, evolutionary understanding is indispensable. Protein interactions data are rapidly accumulating and are suitable for system-level evolutionary analysis. We have analyzed yeast protein interaction network by both mathematical and biological approaches. In this poster presentation, we inferred the evolutionary birth periods of yeast proteins by reconstructing phylogenetic profile. It has been thought that hub proteins that have high connection degree are evolutionary old. But our analysis showed that hub proteins are entirely evolutionary new. We also examined evolutionary processes of protein complexes. It showed that member proteins of complexes were tend to have appeared in the same evolutionary period. Our results suggested that protein interaction network evolved by modules that form the functional unit. We also reconstructed standardized phylogenetic trees and calculated evolutionary rates of yeast proteins. It showed that there is no obvious correlation between evolutionary rates and connection degrees of yeast proteins.

Keywords: Protein interaction network, evolution, modularity, evolutionary rate, connection degrees.

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Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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